The purpose of this research is to determine the effective way of implementation of the control algorithm, as an important functional part of information and control computer systems. The search criterion is the minimum of internal hardware FPGA resources required for the control unit implementation. This criterion allows miniaturization of dimensions, improves reliability by reducing the number of interconnections inside the chip, and ensures the possibility of a compact arrangement of various system components, which is especially important when using the “system-on-chip” design technology. The control unit holds a prominent place in the digital information and control systems. A comparative analysis of two control unit models represented as a finite state machine with either hard or programmable logic was proposed. Advantages and disadvantages of both models were determined according to the peculiarities of the information and control system algorithms, and, it was proved that the FSM model with a programmable logic matched these peculiarities in a greater degree. The purpose of this study was achieved due to the application of the proposed method for the implementation of the FSM with the programmable logic using the embedded memory of the FPGA and ProASIC chips. The main result was a substantial decrease in the LUT number used. The experimental results were obtained applying the chips of the world's top manufacturers - Xilinx, Altera/Intel, Microsemi. The studies were carried out based on the onboard computing complex control algorithm.